Re: [Rdkit-discuss] ETKDG conformation generation algorithm and fullerene-like structures.
Mhh, your choices of test molecules sounds like going from poster child to
archenemy of conformation generation algorithms :-)
-
| Markus Sitzmann
| markus.sitzm...@gmail.com
> On 7. Sep 2017, at 18:59, Jason Biggs wrote:
>
> I've never had success using the ETKDG or KDG methods for fullerenes, when
> trying on C60 it goes for a long time and returns -1. The ETDG method works
> on C60, but fails on your C60H60.
>
> One thing you could try is to embed the hydrogen-suppressed structure, then
> add the hydrogens
>
> RDKit::DGeomHelpers::EmbedParameters params(RDKit::DGeomHelpers::ETDG);
>
> RDKit::DGeomHelpers::EmbedMolecule(*mol, params);
>
> bool explicitOnly = false;
>
> bool addCoords = true;
>
> RDKit::MolOps::addHs(*mol, explicitOnly, addCoords);
>
> seems to work.
>
>
>
>
> Jason Biggs
>
>
>> On Thu, Sep 7, 2017 at 10:49 AM, Dmitry Redkin wrote:
>> Hello all!
>> I've just started to use RDKit, and now I'm trying to generate some 3D
>> conformation for a molecule. ETKDG successfully optimized cyclohexane, so
>> I've tried some more complex example.
>> It was this fullerene-like structure (with all the single bonds and every C
>> atom having H atom attached). I'm attaching it to this email.
>>
>> But whatever I've tried to do with embedding parameters, RDKit whether
>> stalls for several minutes trying to complete operation or just exits with
>> all zero coordinates.
>>
>> Is there any way to generate conformations for this structure? Maybe I did
>> something wrong or there is some flag that can be set to get some result
>> (any result, not necessarily the best one) in a reasonable time?
>>
>> My code is pretty simple, you can see it below.
>>
>>
>> RWMol *mol = MolFileToMol("d:\\temp\\exe32\\full.mol", true, false, false);
>>
>> MolOps::addHs(*mol);
>> DGeomHelpers::EmbedParameters p(DGeomHelpers::ETKDG);
>> p.maxIterations = 100; // if I left it -1, I could not wait long enough for
>> EmbedMolecule to exit.
>> p.useRandomCoords = true;
>> int confid = DGeomHelpers::EmbedMolecule(*((ROMol*)mol), p);
>> MolToMolFile(*((ROMol*)mol), "d:\\temp\\exe32\\full1.mol", true, confid);
>> free(mol);
>>
>>
>>
>> Dmitry Redkin, ACD Inc.
>> red...@acdlabs.ru
>> --
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>>
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Re: [Rdkit-discuss] ETKDG conformation generation algorithm and fullerene-like structures.
Too much symmetry for conformational comparison?
Many or most conformation generators will test new conformations for a
match with previously generated conformations, and will bail out if they
can't exhaust all possibilities.
(I don't know if this is the case RDKit facilities.)
-P.
On Thu, Sep 7, 2017 at 12:59 PM, Jason Biggs wrote:
> I've never had success using the ETKDG or KDG methods for fullerenes,
> when trying on C60 it goes for a long time and returns -1. The ETDG method
> works on C60, but fails on your C60H60.
>
> One thing you could try is to embed the hydrogen-suppressed structure,
> then add the hydrogens
>
> RDKit::DGeomHelpers::EmbedParameters params(RDKit::DGeomHelpers::ETDG);
>
> RDKit::DGeomHelpers::EmbedMolecule(*mol, params);
>
> bool explicitOnly = false;
>
> bool addCoords = true;
>
> RDKit::MolOps::addHs(*mol, explicitOnly, addCoords);
>
> seems to work.
>
>
>
> Jason Biggs
>
>
> On Thu, Sep 7, 2017 at 10:49 AM, Dmitry Redkin wrote:
>
>> Hello all!
>> I've just started to use RDKit, and now I'm trying to generate some 3D
>> conformation for a molecule. ETKDG successfully optimized cyclohexane, so
>> I've tried some more complex example.
>> It was this fullerene-like structure (with all the single bonds and every
>> C
>> atom having H atom attached). I'm attaching it to this email.
>>
>> But whatever I've tried to do with embedding parameters, RDKit whether
>> stalls for several minutes trying to complete operation or just exits with
>> all zero coordinates.
>>
>> Is there any way to generate conformations for this structure? Maybe I did
>> something wrong or there is some flag that can be set to get some result
>> (any result, not necessarily the best one) in a reasonable time?
>>
>> My code is pretty simple, you can see it below.
>>
>>
>> RWMol *mol = MolFileToMol("d:\\temp\\exe32\\full.mol", true, false,
>> false);
>>
>> MolOps::addHs(*mol);
>> DGeomHelpers::EmbedParameters p(DGeomHelpers::ETKDG);
>> p.maxIterations = 100; // if I left it -1, I could not wait long enough
>> for
>> EmbedMolecule to exit.
>> p.useRandomCoords = true;
>> int confid = DGeomHelpers::EmbedMolecule(*((ROMol*)mol), p);
>> MolToMolFile(*((ROMol*)mol), "d:\\temp\\exe32\\full1.mol", true, confid);
>> free(mol);
>>
>>
>>
>> Dmitry Redkin, ACD Inc.
>> red...@acdlabs.ru
>> --
>> This message has been scanned for viruses and
>> dangerous content by MailScanner, and is
>> believed to be clean.
>>
>>
>>
>> --
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>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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>>
>>
>
>
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Re: [Rdkit-discuss] ETKDG conformation generation algorithm and fullerene-like structures.
I've never had success using the ETKDG or KDG methods for fullerenes, when
trying on C60 it goes for a long time and returns -1. The ETDG method
works on C60, but fails on your C60H60.
One thing you could try is to embed the hydrogen-suppressed structure, then
add the hydrogens
RDKit::DGeomHelpers::EmbedParameters params(RDKit::DGeomHelpers::ETDG);
RDKit::DGeomHelpers::EmbedMolecule(*mol, params);
bool explicitOnly = false;
bool addCoords = true;
RDKit::MolOps::addHs(*mol, explicitOnly, addCoords);
seems to work.
Jason Biggs
On Thu, Sep 7, 2017 at 10:49 AM, Dmitry Redkin wrote:
> Hello all!
> I've just started to use RDKit, and now I'm trying to generate some 3D
> conformation for a molecule. ETKDG successfully optimized cyclohexane, so
> I've tried some more complex example.
> It was this fullerene-like structure (with all the single bonds and every C
> atom having H atom attached). I'm attaching it to this email.
>
> But whatever I've tried to do with embedding parameters, RDKit whether
> stalls for several minutes trying to complete operation or just exits with
> all zero coordinates.
>
> Is there any way to generate conformations for this structure? Maybe I did
> something wrong or there is some flag that can be set to get some result
> (any result, not necessarily the best one) in a reasonable time?
>
> My code is pretty simple, you can see it below.
>
>
> RWMol *mol = MolFileToMol("d:\\temp\\exe32\\full.mol", true, false,
> false);
>
> MolOps::addHs(*mol);
> DGeomHelpers::EmbedParameters p(DGeomHelpers::ETKDG);
> p.maxIterations = 100; // if I left it -1, I could not wait long enough for
> EmbedMolecule to exit.
> p.useRandomCoords = true;
> int confid = DGeomHelpers::EmbedMolecule(*((ROMol*)mol), p);
> MolToMolFile(*((ROMol*)mol), "d:\\temp\\exe32\\full1.mol", true, confid);
> free(mol);
>
>
>
> Dmitry Redkin, ACD Inc.
> red...@acdlabs.ru
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
>
>
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
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>
>
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